NM_001080414.4:c.5087T>C
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001080414.4(CCDC88C):c.5087T>C(p.Leu1696Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00163 in 1,485,276 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L1696L) has been classified as Likely benign.
Frequency
Consequence
NM_001080414.4 missense
Scores
Clinical Significance
Conservation
Publications
- hydrocephalus, nonsyndromic, autosomal recessive 1Inheritance: AR Classification: STRONG, MODERATE Submitted by: Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
- spinocerebellar ataxia type 40Inheritance: AD Classification: MODERATE, SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet
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ACMG classification
Our verdict: Benign. The variant received -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.5087T>C | p.Leu1696Pro | missense_variant | Exon 30 of 30 | 5 | NM_001080414.4 | ENSP00000374507.6 | ||
CCDC88C | ENST00000334448.5 | n.899T>C | non_coding_transcript_exon_variant | Exon 6 of 6 | 1 | |||||
CCDC88C | ENST00000556726.5 | c.*921T>C | 3_prime_UTR_variant | Exon 7 of 7 | 5 | ENSP00000452406.1 |
Frequencies
GnomAD3 genomes AF: 0.00207 AC: 315AN: 152196Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00227 AC: 363AN: 160104 AF XY: 0.00262 show subpopulations
GnomAD4 exome AF: 0.00158 AC: 2112AN: 1332962Hom.: 13 Cov.: 34 AF XY: 0.00173 AC XY: 1121AN XY: 649824 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00207 AC: 315AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.00213 AC XY: 159AN XY: 74484 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:2
CCDC88C: BS2 -
- -
not specified Uncertain:1
- -
CCDC88C-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at